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        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/pangenome analysis pipeline. For information about how to interpret these results, please see the documentation.

        Report generated on 2024-04-11, 09:14 CEST based on data in: /tmp/jean/pggb/work/15/1eecc7f3e3c582bb967c4e65351a67

        ODGI

        ODGI is an optimized dynamic graph/genome implementation, for efficient analysis and manipulation of pangenome graphs structured in the variation graph model.

        Detailed ODGI stats table.

        Showing 2/2 rows and 10/14 columns.
        Sample NameLengthNodesEdgesPathsComponentsACTGN
        chrY.hprc.pan4
        57227415
        1
        0
        1
        1
        7155845
        4632232
        7217789
        4630489
        33591060
        seqwish
        57227415
        1
        0
        1
        1
        7155845
        4632232
        7217789
        4630489
        33591060

        Sum of path node distances

        For each path we iterate from node to node and count the node / nucleotide distance of nodes on the pangenome level normalized by the path length. If a node is reversed, we count the node distance twice.

        This value allows you to evaluate the sorting goodness - how linear the graph is.

        Created with MultiQC

        For each path we iterate from node to node and count the node / nucleotide distance mean_links_length of nodes within the same path only. We then normalized by the path length.

        This value allows you to evaluate the sorting goodness - how linear the graph is.

        Error - was not able to plot data.

        ODGI Compressed 1D visualization

        This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. Summarization of path coverage across all paths. A heatmap color-coding from https://colorbrewer2.org/#type=diverging&scheme=RdBu&n=11 is used. Dark blue means highest coverage. Dark red means lowest coverage. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.

        ODGI 1D visualization

        This image shows a 1D rendering of the built pangenome graph. The graph nodes are arranged from left to right, forming the pangenome sequence. The colored bars represent the paths versus the pangenome sequence in a binary matrix. The path names are placed on the left. The black lines under the paths are the links, which represent the graph topology.

        ODGI 1D visualization by path position

        This shows a 1D rendering of the built pangenome graph where the paths are colored according to their nucleotide position. Light grey means a low path position, black is the highest path position.

        ODGI 1D visualization by path orientation

        This image shows a 1D rendering of the built pangenome graph where the paths are colored by orientation. Forward is black, reverse is red.

        ODGI 1D visualization by node depth

        This shows a 1D rendering of the built pangenome graph where the paths are colored according to path depth. Using the Spectra color palette with 4 levels of path depths, white indicates no depth, while grey, red, and yellow indicate depth 1, 2, and greater than or equal to 3, respectively.

        ODGI 1D visualization by uncalled bases

        This shows a 1D rendering of the built pangenome graph where the paths are colored according to the coverage of uncalled bases. The lighter the green, the higher the 'N' content of a node is.

        ODGI 2D drawing

        This image shows a 2D rendering of the built pangenome graph.

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        GFAFFIXgfaffix0.1.5b0
        ODGI_BUILDodgi0.8.4
        ODGI_DRAW_HEIGHTodgi0.8.4
        ODGI_DRAW_MULTIQCodgi0.8.4
        ODGI_LAYOUTodgi0.8.4
        ODGI_SORTodgi0.8.4
        ODGI_STATSodgi0.8.4
        ODGI_UNCHOPodgi0.8.4
        ODGI_VIEWodgi0.8.4
        ODGI_VIZ_COLORodgi0.8.4
        ODGI_VIZ_COMPRodgi0.8.4
        ODGI_VIZ_DEPTHodgi0.8.4
        ODGI_VIZ_INVodgi0.8.4
        ODGI_VIZ_POSodgi0.8.4
        ODGI_VIZ_UNCALLEDodgi0.8.4
        SEQWISHseqwish0.7.9
        SMOOTHXGsmoothxg0.7.2
        SPLIT_APPROX_MAPPINGS_IN_CHUNKSpggbnull
        WFMASH_ALIGNwfmash0.10.4
        WFMASH_MAPwfmash0.10.4
        WorkflowNextflow23.10.1
        nf-core/pangenomev1.1.2-g0e8a387

        nf-core/pangenome Workflow Summary

        - this information is collected when the pipeline is started.

        Core Nextflow options

        revision
        1.1.2
        runName
        stoic_edison
        containerEngine
        singularity
        launchDir
        /tmp/jean/pggb
        workDir
        /tmp/jean/pggb/work
        projectDir
        /tmp/jean/.nextflow/assets/nf-core/pangenome
        userName
        demo
        profile
        singularity
        configFiles
        N/A

        Input/output options

        input
        ../data/chrY.hprc.pan4.fa.gz
        n_haplotypes
        4
        outdir
        chrY.hprc.pan4_out

        Wfmash Options

        wfmash_map_pct_id
        98
        wfmash_segment_length
        10k
        wfmash_exclude_delim
        #
        wfmash_chunks
        4
        wfmash_n_mappings
        3

        Seqwish Options

        seqwish_min_match_length
        311
        seqwish_sparse_factor
        0.0

        Smoothxg options

        smoothxg_poa_length
        1000,

        MultiQC v1.21 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.